1 Data preparation

1.1 Outline

  • Load scripts: loads libraries and useful scripts used in the analyses; all .R files contained in scripts at the root of the factory are automatically loaded

  • Load data: imports datasets, and may contain some ad hoc changes to the data such as specific data cleaning (not used in other reports), new variables used in the analyses, etc.

1.2 Load packages


library(reportfactory)
library(here)
library(rio) 
library(tidyverse)
library(incidence)
library(distcrete)
library(epitrix)
library(earlyR)
library(projections)
library(linelist)
library(remotes)
library(janitor)
library(kableExtra)
library(DT)
library(cyphr)
library(chngpt)
library(lubridate)
library(ggpubr)
library(ggnewscale)

1.3 Load scripts

These scripts will load:

  • all scripts stored as .R files inside /scripts/
  • all scripts stored as .R files inside /src/

These scripts also contain routines to access the latest clean encrypted data (see next section).


reportfactory::rfh_load_scripts()

1.4 Load clean data

We import the latest NHS pathways data:


x <- import_pathways() %>%
  as_tibble()
x
## # A tibble: 408,143 x 11
##    site_type date       sex   age   ccg_code ccg_name count postcode nhs_region
##    <chr>     <date>     <chr> <chr> <chr>    <chr>    <int> <chr>    <chr>     
##  1 111       2020-03-18 fema… miss… e380000… nhs_glo…     1 gl34fe   South West
##  2 111       2020-03-18 fema… miss… e380001… nhs_sou…     1 ne325nn  North Eas…
##  3 111       2020-03-18 fema… 0-18  e380000… nhs_air…     8 bd57jr   North Eas…
##  4 111       2020-03-18 fema… 0-18  e380000… nhs_ash…     7 tn254ab  South East
##  5 111       2020-03-18 fema… 0-18  e380000… nhs_bar…    35 rm13ae   London    
##  6 111       2020-03-18 fema… 0-18  e380000… nhs_bar…     9 n111np   London    
##  7 111       2020-03-18 fema… 0-18  e380000… nhs_bar…    11 s752py   North Eas…
##  8 111       2020-03-18 fema… 0-18  e380000… nhs_bas…    19 ss143hg  East of E…
##  9 111       2020-03-18 fema… 0-18  e380000… nhs_bas…     6 dn227xf  North Eas…
## 10 111       2020-03-18 fema… 0-18  e380000… nhs_bat…     9 ba25rp   South West
## # … with 408,133 more rows, and 2 more variables: day <int>, weekday <fct>

We also import demographics data for NHS regions in England, used later in our analysis:


path <- here::here("data", "csv", "nhs_region_population_2018.csv")
nhs_region_pop <- rio::import(path) %>%
  mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))

nhs_region_pop$nhs_region <- gsub(" Of ", " of ", nhs_region_pop$nhs_region)
nhs_region_pop$nhs_region <- gsub(" And ", " and ", nhs_region_pop$nhs_region)
nhs_region_pop
##                  nhs_region variable      value
## 1                North West     0-18 0.22538599
## 2  North East and Yorkshire     0-18 0.21876449
## 3                  Midlands     0-18 0.22564656
## 4           East of England     0-18 0.22810783
## 5                    London     0-18 0.23764782
## 6                South East     0-18 0.22458811
## 7                South West     0-18 0.20799797
## 8                North West    19-69 0.64274078
## 9  North East and Yorkshire    19-69 0.64437753
## 10                 Midlands    19-69 0.63876675
## 11          East of England    19-69 0.63034229
## 12                   London    19-69 0.67820084
## 13               South East    19-69 0.63267336
## 14               South West    19-69 0.63176131
## 15               North West   70-120 0.13187323
## 16 North East and Yorkshire   70-120 0.13685797
## 17                 Midlands   70-120 0.13558669
## 18          East of England   70-120 0.14154988
## 19                   London   70-120 0.08415135
## 20               South East   70-120 0.14273853
## 21               South West   70-120 0.16024072

Finally, we import publically available deaths per NHS region:


dth <- import_deaths() %>%
  mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))

#truncation to account for reporting delay
delay_max <- 21

dth$nhs_region <- gsub(" Of ", " of ", dth$nhs_region)
dth$nhs_region <- gsub(" And ", " and ", dth$nhs_region)
dth
##      date_report               nhs_region deaths
## 1     2020-03-01          East of England      0
## 2     2020-03-02          East of England      1
## 3     2020-03-03          East of England      0
## 4     2020-03-04          East of England      0
## 5     2020-03-05          East of England      0
## 6     2020-03-06          East of England      1
## 7     2020-03-07          East of England      0
## 8     2020-03-08          East of England      0
## 9     2020-03-09          East of England      1
## 10    2020-03-10          East of England      0
## 11    2020-03-11          East of England      0
## 12    2020-03-12          East of England      0
## 13    2020-03-13          East of England      1
## 14    2020-03-14          East of England      2
## 15    2020-03-15          East of England      2
## 16    2020-03-16          East of England      1
## 17    2020-03-17          East of England      1
## 18    2020-03-18          East of England      5
## 19    2020-03-19          East of England      4
## 20    2020-03-20          East of England      2
## 21    2020-03-21          East of England     11
## 22    2020-03-22          East of England     12
## 23    2020-03-23          East of England     11
## 24    2020-03-24          East of England     19
## 25    2020-03-25          East of England     26
## 26    2020-03-26          East of England     36
## 27    2020-03-27          East of England     38
## 28    2020-03-28          East of England     28
## 29    2020-03-29          East of England     43
## 30    2020-03-30          East of England     45
## 31    2020-03-31          East of England     70
## 32    2020-04-01          East of England     62
## 33    2020-04-02          East of England     65
## 34    2020-04-03          East of England     80
## 35    2020-04-04          East of England     71
## 36    2020-04-05          East of England     76
## 37    2020-04-06          East of England     71
## 38    2020-04-07          East of England     93
## 39    2020-04-08          East of England    111
## 40    2020-04-09          East of England     87
## 41    2020-04-10          East of England     74
## 42    2020-04-11          East of England     92
## 43    2020-04-12          East of England    100
## 44    2020-04-13          East of England     78
## 45    2020-04-14          East of England     61
## 46    2020-04-15          East of England     82
## 47    2020-04-16          East of England     74
## 48    2020-04-17          East of England     86
## 49    2020-04-18          East of England     64
## 50    2020-04-19          East of England     67
## 51    2020-04-20          East of England     67
## 52    2020-04-21          East of England     75
## 53    2020-04-22          East of England     67
## 54    2020-04-23          East of England     49
## 55    2020-04-24          East of England     66
## 56    2020-04-25          East of England     54
## 57    2020-04-26          East of England     48
## 58    2020-04-27          East of England     46
## 59    2020-04-28          East of England     58
## 60    2020-04-29          East of England     32
## 61    2020-04-30          East of England     45
## 62    2020-05-01          East of England     49
## 63    2020-05-02          East of England     29
## 64    2020-05-03          East of England     41
## 65    2020-05-04          East of England     19
## 66    2020-05-05          East of England     36
## 67    2020-05-06          East of England     31
## 68    2020-05-07          East of England     33
## 69    2020-05-08          East of England     33
## 70    2020-05-09          East of England     29
## 71    2020-05-10          East of England     22
## 72    2020-05-11          East of England     18
## 73    2020-05-12          East of England     21
## 74    2020-05-13          East of England     27
## 75    2020-05-14          East of England     26
## 76    2020-05-15          East of England     19
## 77    2020-05-16          East of England     26
## 78    2020-05-17          East of England     17
## 79    2020-05-18          East of England     25
## 80    2020-05-19          East of England     15
## 81    2020-05-20          East of England     26
## 82    2020-05-21          East of England     21
## 83    2020-05-22          East of England     13
## 84    2020-05-23          East of England     12
## 85    2020-05-24          East of England     17
## 86    2020-05-25          East of England     25
## 87    2020-05-26          East of England     14
## 88    2020-05-27          East of England     12
## 89    2020-05-28          East of England     17
## 90    2020-05-29          East of England     16
## 91    2020-05-30          East of England      9
## 92    2020-05-31          East of England      8
## 93    2020-06-01          East of England     17
## 94    2020-06-02          East of England     14
## 95    2020-06-03          East of England     10
## 96    2020-06-04          East of England      7
## 97    2020-06-05          East of England     14
## 98    2020-06-06          East of England      5
## 99    2020-06-07          East of England      9
## 100   2020-06-08          East of England      7
## 101   2020-06-09          East of England      6
## 102   2020-06-10          East of England      8
## 103   2020-06-11          East of England      1
## 104   2020-06-12          East of England      9
## 105   2020-06-13          East of England      5
## 106   2020-06-14          East of England      4
## 107   2020-06-15          East of England      8
## 108   2020-06-16          East of England      3
## 109   2020-06-17          East of England      7
## 110   2020-06-18          East of England      4
## 111   2020-06-19          East of England      7
## 112   2020-06-20          East of England      4
## 113   2020-06-21          East of England      3
## 114   2020-06-22          East of England      6
## 115   2020-06-23          East of England      5
## 116   2020-06-24          East of England      4
## 117   2020-06-25          East of England      1
## 118   2020-06-26          East of England      5
## 119   2020-06-27          East of England      6
## 120   2020-06-28          East of England      8
## 121   2020-06-29          East of England      4
## 122   2020-06-30          East of England      5
## 123   2020-07-01          East of England      2
## 124   2020-07-02          East of England      5
## 125   2020-07-03          East of England      0
## 126   2020-07-04          East of England      3
## 127   2020-07-05          East of England      1
## 128   2020-07-06          East of England      2
## 129   2020-07-07          East of England      2
## 130   2020-07-08          East of England      0
## 131   2020-07-09          East of England      8
## 132   2020-07-10          East of England      4
## 133   2020-07-11          East of England      2
## 134   2020-07-12          East of England      1
## 135   2020-07-13          East of England      8
## 136   2020-07-14          East of England      2
## 137   2020-07-15          East of England      0
## 138   2020-07-16          East of England      0
## 139   2020-07-17          East of England      0
## 140   2020-07-18          East of England      0
## 141   2020-07-19          East of England      1
## 142   2020-07-20          East of England      1
## 143   2020-07-21          East of England      1
## 144   2020-07-22          East of England      2
## 145   2020-07-23          East of England      1
## 146   2020-07-24          East of England      1
## 147   2020-07-25          East of England      0
## 148   2020-07-26          East of England      1
## 149   2020-07-27          East of England      1
## 150   2020-07-28          East of England      2
## 151   2020-07-29          East of England      0
## 152   2020-07-30          East of England      0
## 153   2020-07-31          East of England      1
## 154   2020-08-01          East of England      0
## 155   2020-08-02          East of England      0
## 156   2020-08-03          East of England      0
## 157   2020-08-04          East of England      1
## 158   2020-08-05          East of England      1
## 159   2020-08-06          East of England      0
## 160   2020-08-07          East of England      1
## 161   2020-08-08          East of England      0
## 162   2020-08-09          East of England      0
## 163   2020-08-10          East of England      1
## 164   2020-08-11          East of England      2
## 165   2020-08-12          East of England      1
## 166   2020-08-13          East of England      0
## 167   2020-08-14          East of England      1
## 168   2020-08-15          East of England      1
## 169   2020-08-16          East of England      0
## 170   2020-08-17          East of England      0
## 171   2020-08-18          East of England      2
## 172   2020-08-19          East of England      1
## 173   2020-08-20          East of England      1
## 174   2020-08-21          East of England      0
## 175   2020-08-22          East of England      1
## 176   2020-08-23          East of England      1
## 177   2020-08-24          East of England      0
## 178   2020-08-25          East of England      0
## 179   2020-08-26          East of England      1
## 180   2020-08-27          East of England      1
## 181   2020-08-28          East of England      0
## 182   2020-08-29          East of England      0
## 183   2020-08-30          East of England      0
## 184   2020-08-31          East of England      0
## 185   2020-09-01          East of England      0
## 186   2020-09-02          East of England      0
## 187   2020-09-03          East of England      1
## 188   2020-09-04          East of England      1
## 189   2020-09-05          East of England      0
## 190   2020-09-06          East of England      1
## 191   2020-09-07          East of England      0
## 192   2020-09-08          East of England      0
## 193   2020-09-09          East of England      0
## 194   2020-09-10          East of England      0
## 195   2020-09-11          East of England      0
## 196   2020-09-12          East of England      0
## 197   2020-09-13          East of England      1
## 198   2020-09-14          East of England      1
## 199   2020-09-15          East of England      0
## 200   2020-09-16          East of England      0
## 201   2020-09-17          East of England      0
## 202   2020-09-18          East of England      0
## 203   2020-09-19          East of England      0
## 204   2020-09-20          East of England      2
## 205   2020-09-21          East of England      0
## 206   2020-09-22          East of England      2
## 207   2020-09-23          East of England      1
## 208   2020-09-24          East of England      0
## 209   2020-09-25          East of England      1
## 210   2020-09-26          East of England      1
## 211   2020-09-27          East of England      1
## 212   2020-09-28          East of England      2
## 213   2020-09-29          East of England      2
## 214   2020-09-30          East of England      2
## 215   2020-10-01          East of England      2
## 216   2020-10-02          East of England      1
## 217   2020-10-03          East of England      1
## 218   2020-10-04          East of England      0
## 219   2020-10-05          East of England      0
## 220   2020-10-06          East of England      4
## 221   2020-10-07          East of England      6
## 222   2020-10-08          East of England      3
## 223   2020-10-09          East of England      1
## 224   2020-10-10          East of England      6
## 225   2020-10-11          East of England      2
## 226   2020-10-12          East of England      2
## 227   2020-10-13          East of England      1
## 228   2020-10-14          East of England      3
## 229   2020-10-15          East of England      4
## 230   2020-10-16          East of England      5
## 231   2020-10-17          East of England      6
## 232   2020-10-18          East of England      7
## 233   2020-10-19          East of England      5
## 234   2020-10-20          East of England      9
## 235   2020-10-21          East of England      7
## 236   2020-10-22          East of England      7
## 237   2020-10-23          East of England     14
## 238   2020-10-24          East of England      1
## 239   2020-10-25          East of England     10
## 240   2020-10-26          East of England     10
## 241   2020-10-27          East of England      8
## 242   2020-10-28          East of England     12
## 243   2020-10-29          East of England     10
## 244   2020-10-30          East of England     12
## 245   2020-10-31          East of England     15
## 246   2020-11-01          East of England     14
## 247   2020-11-02          East of England      9
## 248   2020-11-03          East of England     14
## 249   2020-11-04          East of England     11
## 250   2020-11-05          East of England     12
## 251   2020-11-06          East of England     18
## 252   2020-11-07          East of England     10
## 253   2020-11-08          East of England     13
## 254   2020-11-09          East of England     16
## 255   2020-11-10          East of England     26
## 256   2020-11-11          East of England     14
## 257   2020-11-12          East of England     14
## 258   2020-11-13          East of England     21
## 259   2020-11-14          East of England     19
## 260   2020-11-15          East of England     13
## 261   2020-11-16          East of England     11
## 262   2020-11-17          East of England     17
## 263   2020-11-18          East of England     19
## 264   2020-11-19          East of England     23
## 265   2020-11-20          East of England     24
## 266   2020-11-21          East of England     19
## 267   2020-11-22          East of England     21
## 268   2020-11-23          East of England     18
## 269   2020-11-24          East of England     21
## 270   2020-11-25          East of England     19
## 271   2020-11-26          East of England     19
## 272   2020-11-27          East of England     14
## 273   2020-11-28          East of England     28
## 274   2020-11-29          East of England     19
## 275   2020-11-30          East of England     22
## 276   2020-12-01          East of England     25
## 277   2020-12-02          East of England     18
## 278   2020-12-03          East of England     23
## 279   2020-12-04          East of England     24
## 280   2020-12-05          East of England     25
## 281   2020-12-06          East of England     21
## 282   2020-12-07          East of England     16
## 283   2020-12-08          East of England     26
## 284   2020-12-09          East of England     19
## 285   2020-12-10          East of England     32
## 286   2020-12-11          East of England     32
## 287   2020-12-12          East of England     27
## 288   2020-12-13          East of England     24
## 289   2020-12-14          East of England     31
## 290   2020-12-15          East of England     35
## 291   2020-12-16          East of England     29
## 292   2020-12-17          East of England     41
## 293   2020-12-18          East of England     44
## 294   2020-12-19          East of England     54
## 295   2020-12-20          East of England     50
## 296   2020-12-21          East of England     63
## 297   2020-12-22          East of England     52
## 298   2020-12-23          East of England     60
## 299   2020-12-24          East of England     54
## 300   2020-12-25          East of England     56
## 301   2020-12-26          East of England     61
## 302   2020-12-27          East of England     53
## 303   2020-12-28          East of England     70
## 304   2020-12-29          East of England     49
## 305   2020-12-30          East of England     68
## 306   2020-12-31          East of England     79
## 307   2021-01-01          East of England     85
## 308   2021-01-02          East of England     63
## 309   2021-01-03          East of England     74
## 310   2021-01-04          East of England     79
## 311   2021-01-05          East of England     99
## 312   2021-01-06          East of England     88
## 313   2021-01-07          East of England    107
## 314   2021-01-08          East of England     82
## 315   2021-01-09          East of England    114
## 316   2021-01-10          East of England    112
## 317   2021-01-11          East of England    111
## 318   2021-01-12          East of England    103
## 319   2021-01-13          East of England    102
## 320   2021-01-14          East of England     78
## 321   2021-01-15          East of England     61
## 322   2021-01-16          East of England     39
## 323   2021-01-17          East of England      8
## 324   2020-03-01                   London      0
## 325   2020-03-02                   London      0
## 326   2020-03-03                   London      0
## 327   2020-03-04                   London      0
## 328   2020-03-05                   London      0
## 329   2020-03-06                   London      1
## 330   2020-03-07                   London      0
## 331   2020-03-08                   London      0
## 332   2020-03-09                   London      1
## 333   2020-03-10                   London      0
## 334   2020-03-11                   London      5
## 335   2020-03-12                   London      6
## 336   2020-03-13                   London     10
## 337   2020-03-14                   London     13
## 338   2020-03-15                   London      9
## 339   2020-03-16                   London     15
## 340   2020-03-17                   London     23
## 341   2020-03-18                   London     28
## 342   2020-03-19                   London     25
## 343   2020-03-20                   London     44
## 344   2020-03-21                   London     49
## 345   2020-03-22                   London     54
## 346   2020-03-23                   London     63
## 347   2020-03-24                   London     86
## 348   2020-03-25                   London    112
## 349   2020-03-26                   London    130
## 350   2020-03-27                   London    130
## 351   2020-03-28                   London    123
## 352   2020-03-29                   London    145
## 353   2020-03-30                   London    151
## 354   2020-03-31                   London    183
## 355   2020-04-01                   London    202
## 356   2020-04-02                   London    191
## 357   2020-04-03                   London    199
## 358   2020-04-04                   London    231
## 359   2020-04-05                   London    195
## 360   2020-04-06                   London    198
## 361   2020-04-07                   London    220
## 362   2020-04-08                   London    239
## 363   2020-04-09                   London    207
## 364   2020-04-10                   London    171
## 365   2020-04-11                   London    178
## 366   2020-04-12                   London    159
## 367   2020-04-13                   London    166
## 368   2020-04-14                   London    143
## 369   2020-04-15                   London    143
## 370   2020-04-16                   London    140
## 371   2020-04-17                   London    101
## 372   2020-04-18                   London    101
## 373   2020-04-19                   London    103
## 374   2020-04-20                   London     96
## 375   2020-04-21                   London     96
## 376   2020-04-22                   London    109
## 377   2020-04-23                   London     77
## 378   2020-04-24                   London     71
## 379   2020-04-25                   London     58
## 380   2020-04-26                   London     53
## 381   2020-04-27                   London     52
## 382   2020-04-28                   London     44
## 383   2020-04-29                   London     45
## 384   2020-04-30                   London     40
## 385   2020-05-01                   London     41
## 386   2020-05-02                   London     41
## 387   2020-05-03                   London     36
## 388   2020-05-04                   London     30
## 389   2020-05-05                   London     25
## 390   2020-05-06                   London     37
## 391   2020-05-07                   London     37
## 392   2020-05-08                   London     31
## 393   2020-05-09                   London     23
## 394   2020-05-10                   London     26
## 395   2020-05-11                   London     18
## 396   2020-05-12                   London     18
## 397   2020-05-13                   London     17
## 398   2020-05-14                   London     20
## 399   2020-05-15                   London     19
## 400   2020-05-16                   London     14
## 401   2020-05-17                   London     15
## 402   2020-05-18                   London     11
## 403   2020-05-19                   London     14
## 404   2020-05-20                   London     19
## 405   2020-05-21                   London     12
## 406   2020-05-22                   London     10
## 407   2020-05-23                   London      6
## 408   2020-05-24                   London      7
## 409   2020-05-25                   London      9
## 410   2020-05-26                   London     14
## 411   2020-05-27                   London      7
## 412   2020-05-28                   London      8
## 413   2020-05-29                   London      7
## 414   2020-05-30                   London     12
## 415   2020-05-31                   London      6
## 416   2020-06-01                   London     10
## 417   2020-06-02                   London      8
## 418   2020-06-03                   London      6
## 419   2020-06-04                   London      8
## 420   2020-06-05                   London      4
## 421   2020-06-06                   London      0
## 422   2020-06-07                   London      5
## 423   2020-06-08                   London      5
## 424   2020-06-09                   London      5
## 425   2020-06-10                   London      8
## 426   2020-06-11                   London      5
## 427   2020-06-12                   London      3
## 428   2020-06-13                   London      3
## 429   2020-06-14                   London      3
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## 966   2021-01-14                 Midlands    144
## 967   2021-01-15                 Midlands     93
## 968   2021-01-16                 Midlands     87
## 969   2021-01-17                 Midlands     12
## 970   2020-03-01 North East and Yorkshire      0
## 971   2020-03-02 North East and Yorkshire      0
## 972   2020-03-03 North East and Yorkshire      0
## 973   2020-03-04 North East and Yorkshire      0
## 974   2020-03-05 North East and Yorkshire      0
## 975   2020-03-06 North East and Yorkshire      0
## 976   2020-03-07 North East and Yorkshire      0
## 977   2020-03-08 North East and Yorkshire      0
## 978   2020-03-09 North East and Yorkshire      0
## 979   2020-03-10 North East and Yorkshire      0
## 980   2020-03-11 North East and Yorkshire      0
## 981   2020-03-12 North East and Yorkshire      0
## 982   2020-03-13 North East and Yorkshire      0
## 983   2020-03-14 North East and Yorkshire      0
## 984   2020-03-15 North East and Yorkshire      2
## 985   2020-03-16 North East and Yorkshire      3
## 986   2020-03-17 North East and Yorkshire      1
## 987   2020-03-18 North East and Yorkshire      2
## 988   2020-03-19 North East and Yorkshire      6
## 989   2020-03-20 North East and Yorkshire      5
## 990   2020-03-21 North East and Yorkshire      6
## 991   2020-03-22 North East and Yorkshire      7
## 992   2020-03-23 North East and Yorkshire      9
## 993   2020-03-24 North East and Yorkshire      8
## 994   2020-03-25 North East and Yorkshire     18
## 995   2020-03-26 North East and Yorkshire     21
## 996   2020-03-27 North East and Yorkshire     28
## 997   2020-03-28 North East and Yorkshire     35
## 998   2020-03-29 North East and Yorkshire     38
## 999   2020-03-30 North East and Yorkshire     64
## 1000  2020-03-31 North East and Yorkshire     60
## 1001  2020-04-01 North East and Yorkshire     67
## 1002  2020-04-02 North East and Yorkshire     75
## 1003  2020-04-03 North East and Yorkshire    100
## 1004  2020-04-04 North East and Yorkshire    105
## 1005  2020-04-05 North East and Yorkshire     92
## 1006  2020-04-06 North East and Yorkshire     96
## 1007  2020-04-07 North East and Yorkshire    102
## 1008  2020-04-08 North East and Yorkshire    107
## 1009  2020-04-09 North East and Yorkshire    111
## 1010  2020-04-10 North East and Yorkshire    117
## 1011  2020-04-11 North East and Yorkshire     98
## 1012  2020-04-12 North East and Yorkshire     84
## 1013  2020-04-13 North East and Yorkshire     94
## 1014  2020-04-14 North East and Yorkshire    107
## 1015  2020-04-15 North East and Yorkshire     96
## 1016  2020-04-16 North East and Yorkshire    103
## 1017  2020-04-17 North East and Yorkshire     88
## 1018  2020-04-18 North East and Yorkshire     95
## 1019  2020-04-19 North East and Yorkshire     88
## 1020  2020-04-20 North East and Yorkshire    100
## 1021  2020-04-21 North East and Yorkshire     76
## 1022  2020-04-22 North East and Yorkshire     84
## 1023  2020-04-23 North East and Yorkshire     63
## 1024  2020-04-24 North East and Yorkshire     72
## 1025  2020-04-25 North East and Yorkshire     69
## 1026  2020-04-26 North East and Yorkshire     65
## 1027  2020-04-27 North East and Yorkshire     65
## 1028  2020-04-28 North East and Yorkshire     57
## 1029  2020-04-29 North East and Yorkshire     69
## 1030  2020-04-30 North East and Yorkshire     57
## 1031  2020-05-01 North East and Yorkshire     64
## 1032  2020-05-02 North East and Yorkshire     48
## 1033  2020-05-03 North East and Yorkshire     40
## 1034  2020-05-04 North East and Yorkshire     49
## 1035  2020-05-05 North East and Yorkshire     40
## 1036  2020-05-06 North East and Yorkshire     51
## 1037  2020-05-07 North East and Yorkshire     45
## 1038  2020-05-08 North East and Yorkshire     42
## 1039  2020-05-09 North East and Yorkshire     44
## 1040  2020-05-10 North East and Yorkshire     40
## 1041  2020-05-11 North East and Yorkshire     29
## 1042  2020-05-12 North East and Yorkshire     27
## 1043  2020-05-13 North East and Yorkshire     28
## 1044  2020-05-14 North East and Yorkshire     31
## 1045  2020-05-15 North East and Yorkshire     32
## 1046  2020-05-16 North East and Yorkshire     35
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## 1048  2020-05-18 North East and Yorkshire     30
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## 1052  2020-05-22 North East and Yorkshire     22
## 1053  2020-05-23 North East and Yorkshire     18
## 1054  2020-05-24 North East and Yorkshire     26
## 1055  2020-05-25 North East and Yorkshire     21
## 1056  2020-05-26 North East and Yorkshire     21
## 1057  2020-05-27 North East and Yorkshire     22
## 1058  2020-05-28 North East and Yorkshire     21
## 1059  2020-05-29 North East and Yorkshire     25
## 1060  2020-05-30 North East and Yorkshire     20
## 1061  2020-05-31 North East and Yorkshire     20
## 1062  2020-06-01 North East and Yorkshire     17
## 1063  2020-06-02 North East and Yorkshire     23
## 1064  2020-06-03 North East and Yorkshire     24
## 1065  2020-06-04 North East and Yorkshire     17
## 1066  2020-06-05 North East and Yorkshire     18
## 1067  2020-06-06 North East and Yorkshire     21
## 1068  2020-06-07 North East and Yorkshire     14
## 1069  2020-06-08 North East and Yorkshire     11
## 1070  2020-06-09 North East and Yorkshire     12
## 1071  2020-06-10 North East and Yorkshire     19
## 1072  2020-06-11 North East and Yorkshire      7
## 1073  2020-06-12 North East and Yorkshire      9
## 1074  2020-06-13 North East and Yorkshire     10
## 1075  2020-06-14 North East and Yorkshire     11
## 1076  2020-06-15 North East and Yorkshire      9
## 1077  2020-06-16 North East and Yorkshire     10
## 1078  2020-06-17 North East and Yorkshire      9
## 1079  2020-06-18 North East and Yorkshire     11
## 1080  2020-06-19 North East and Yorkshire      6
## 1081  2020-06-20 North East and Yorkshire      5
## 1082  2020-06-21 North East and Yorkshire      4
## 1083  2020-06-22 North East and Yorkshire      7
## 1084  2020-06-23 North East and Yorkshire      8
## 1085  2020-06-24 North East and Yorkshire     10
## 1086  2020-06-25 North East and Yorkshire      4
## 1087  2020-06-26 North East and Yorkshire      8
## 1088  2020-06-27 North East and Yorkshire      4
## 1089  2020-06-28 North East and Yorkshire      5
## 1090  2020-06-29 North East and Yorkshire      2
## 1091  2020-06-30 North East and Yorkshire      7
## 1092  2020-07-01 North East and Yorkshire      1
## 1093  2020-07-02 North East and Yorkshire      5
## 1094  2020-07-03 North East and Yorkshire      4
## 1095  2020-07-04 North East and Yorkshire      4
## 1096  2020-07-05 North East and Yorkshire      3
## 1097  2020-07-06 North East and Yorkshire      2
## 1098  2020-07-07 North East and Yorkshire      3
## 1099  2020-07-08 North East and Yorkshire      3
## 1100  2020-07-09 North East and Yorkshire      0
## 1101  2020-07-10 North East and Yorkshire      3
## 1102  2020-07-11 North East and Yorkshire      1
## 1103  2020-07-12 North East and Yorkshire      4
## 1104  2020-07-13 North East and Yorkshire      1
## 1105  2020-07-14 North East and Yorkshire      1
## 1106  2020-07-15 North East and Yorkshire      2
## 1107  2020-07-16 North East and Yorkshire      3
## 1108  2020-07-17 North East and Yorkshire      1
## 1109  2020-07-18 North East and Yorkshire      2
## 1110  2020-07-19 North East and Yorkshire      2
## 1111  2020-07-20 North East and Yorkshire      1
## 1112  2020-07-21 North East and Yorkshire      1
## 1113  2020-07-22 North East and Yorkshire      6
## 1114  2020-07-23 North East and Yorkshire      0
## 1115  2020-07-24 North East and Yorkshire      1
## 1116  2020-07-25 North East and Yorkshire      5
## 1117  2020-07-26 North East and Yorkshire      1
## 1118  2020-07-27 North East and Yorkshire      0
## 1119  2020-07-28 North East and Yorkshire      2
## 1120  2020-07-29 North East and Yorkshire      1
## 1121  2020-07-30 North East and Yorkshire      0
## 1122  2020-07-31 North East and Yorkshire      1
## 1123  2020-08-01 North East and Yorkshire      3
## 1124  2020-08-02 North East and Yorkshire      2
## 1125  2020-08-03 North East and Yorkshire      1
## 1126  2020-08-04 North East and Yorkshire      3
## 1127  2020-08-05 North East and Yorkshire      1
## 1128  2020-08-06 North East and Yorkshire      4
## 1129  2020-08-07 North East and Yorkshire      0
## 1130  2020-08-08 North East and Yorkshire      2
## 1131  2020-08-09 North East and Yorkshire      3
## 1132  2020-08-10 North East and Yorkshire      3
## 1133  2020-08-11 North East and Yorkshire      2
## 1134  2020-08-12 North East and Yorkshire      2
## 1135  2020-08-13 North East and Yorkshire      0
## 1136  2020-08-14 North East and Yorkshire      1
## 1137  2020-08-15 North East and Yorkshire      1
## 1138  2020-08-16 North East and Yorkshire      0
## 1139  2020-08-17 North East and Yorkshire      6
## 1140  2020-08-18 North East and Yorkshire      1
## 1141  2020-08-19 North East and Yorkshire      0
## 1142  2020-08-20 North East and Yorkshire      0
## 1143  2020-08-21 North East and Yorkshire      1
## 1144  2020-08-22 North East and Yorkshire      1
## 1145  2020-08-23 North East and Yorkshire      3
## 1146  2020-08-24 North East and Yorkshire      0
## 1147  2020-08-25 North East and Yorkshire      2
## 1148  2020-08-26 North East and Yorkshire      2
## 1149  2020-08-27 North East and Yorkshire      1
## 1150  2020-08-28 North East and Yorkshire      0
## 1151  2020-08-29 North East and Yorkshire      1
## 1152  2020-08-30 North East and Yorkshire      0
## 1153  2020-08-31 North East and Yorkshire      0
## 1154  2020-09-01 North East and Yorkshire      2
## 1155  2020-09-02 North East and Yorkshire      3
## 1156  2020-09-03 North East and Yorkshire      1
## 1157  2020-09-04 North East and Yorkshire      1
## 1158  2020-09-05 North East and Yorkshire      2
## 1159  2020-09-06 North East and Yorkshire      1
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## 1161  2020-09-08 North East and Yorkshire      1
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## 1163  2020-09-10 North East and Yorkshire      0
## 1164  2020-09-11 North East and Yorkshire      3
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## 1166  2020-09-13 North East and Yorkshire      3
## 1167  2020-09-14 North East and Yorkshire      4
## 1168  2020-09-15 North East and Yorkshire      3
## 1169  2020-09-16 North East and Yorkshire      3
## 1170  2020-09-17 North East and Yorkshire      5
## 1171  2020-09-18 North East and Yorkshire      6
## 1172  2020-09-19 North East and Yorkshire      2
## 1173  2020-09-20 North East and Yorkshire      9
## 1174  2020-09-21 North East and Yorkshire      7
## 1175  2020-09-22 North East and Yorkshire      5
## 1176  2020-09-23 North East and Yorkshire      6
## 1177  2020-09-24 North East and Yorkshire      3
## 1178  2020-09-25 North East and Yorkshire      5
## 1179  2020-09-26 North East and Yorkshire      7
## 1180  2020-09-27 North East and Yorkshire     10
## 1181  2020-09-28 North East and Yorkshire      6
## 1182  2020-09-29 North East and Yorkshire      7
## 1183  2020-09-30 North East and Yorkshire      7
## 1184  2020-10-01 North East and Yorkshire      8
## 1185  2020-10-02 North East and Yorkshire     16
## 1186  2020-10-03 North East and Yorkshire     12
## 1187  2020-10-04 North East and Yorkshire     13
## 1188  2020-10-05 North East and Yorkshire     10
## 1189  2020-10-06 North East and Yorkshire     15
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## 1191  2020-10-08 North East and Yorkshire     16
## 1192  2020-10-09 North East and Yorkshire     10
## 1193  2020-10-10 North East and Yorkshire     16
## 1194  2020-10-11 North East and Yorkshire     16
## 1195  2020-10-12 North East and Yorkshire     15
## 1196  2020-10-13 North East and Yorkshire     21
## 1197  2020-10-14 North East and Yorkshire     20
## 1198  2020-10-15 North East and Yorkshire     23
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## 1200  2020-10-17 North East and Yorkshire     34
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## 1203  2020-10-20 North East and Yorkshire     36
## 1204  2020-10-21 North East and Yorkshire     42
## 1205  2020-10-22 North East and Yorkshire     33
## 1206  2020-10-23 North East and Yorkshire     31
## 1207  2020-10-24 North East and Yorkshire     34
## 1208  2020-10-25 North East and Yorkshire     35
## 1209  2020-10-26 North East and Yorkshire     45
## 1210  2020-10-27 North East and Yorkshire     45
## 1211  2020-10-28 North East and Yorkshire     39
## 1212  2020-10-29 North East and Yorkshire     51
## 1213  2020-10-30 North East and Yorkshire     48
## 1214  2020-10-31 North East and Yorkshire     58
## 1215  2020-11-01 North East and Yorkshire     48
## 1216  2020-11-02 North East and Yorkshire     50
## 1217  2020-11-03 North East and Yorkshire     48
## 1218  2020-11-04 North East and Yorkshire     57
## 1219  2020-11-05 North East and Yorkshire     57
## 1220  2020-11-06 North East and Yorkshire     57
## 1221  2020-11-07 North East and Yorkshire     75
## 1222  2020-11-08 North East and Yorkshire     61
## 1223  2020-11-09 North East and Yorkshire     87
## 1224  2020-11-10 North East and Yorkshire     65
## 1225  2020-11-11 North East and Yorkshire     59
## 1226  2020-11-12 North East and Yorkshire     77
## 1227  2020-11-13 North East and Yorkshire     78
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## 1230  2020-11-16 North East and Yorkshire     51
## 1231  2020-11-17 North East and Yorkshire     68
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## 1236  2020-11-22 North East and Yorkshire     80
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## 1240  2020-11-26 North East and Yorkshire     64
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## 1242  2020-11-28 North East and Yorkshire     76
## 1243  2020-11-29 North East and Yorkshire     61
## 1244  2020-11-30 North East and Yorkshire     55
## 1245  2020-12-01 North East and Yorkshire     44
## 1246  2020-12-02 North East and Yorkshire     59
## 1247  2020-12-03 North East and Yorkshire     71
## 1248  2020-12-04 North East and Yorkshire     64
## 1249  2020-12-05 North East and Yorkshire     48
## 1250  2020-12-06 North East and Yorkshire     63
## 1251  2020-12-07 North East and Yorkshire     49
## 1252  2020-12-08 North East and Yorkshire     54
## 1253  2020-12-09 North East and Yorkshire     49
## 1254  2020-12-10 North East and Yorkshire     55
## 1255  2020-12-11 North East and Yorkshire     55
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## 1257  2020-12-13 North East and Yorkshire     51
## 1258  2020-12-14 North East and Yorkshire     49
## 1259  2020-12-15 North East and Yorkshire     54
## 1260  2020-12-16 North East and Yorkshire     40
## 1261  2020-12-17 North East and Yorkshire     49
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## 1265  2020-12-21 North East and Yorkshire     35
## 1266  2020-12-22 North East and Yorkshire     57
## 1267  2020-12-23 North East and Yorkshire     56
## 1268  2020-12-24 North East and Yorkshire     48
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## 1270  2020-12-26 North East and Yorkshire     65
## 1271  2020-12-27 North East and Yorkshire     67
## 1272  2020-12-28 North East and Yorkshire     61
## 1273  2020-12-29 North East and Yorkshire     57
## 1274  2020-12-30 North East and Yorkshire     41
## 1275  2020-12-31 North East and Yorkshire     47
## 1276  2021-01-01 North East and Yorkshire     68
## 1277  2021-01-02 North East and Yorkshire     55
## 1278  2021-01-03 North East and Yorkshire     48
## 1279  2021-01-04 North East and Yorkshire     61
## 1280  2021-01-05 North East and Yorkshire     61
## 1281  2021-01-06 North East and Yorkshire     57
## 1282  2021-01-07 North East and Yorkshire     66
## 1283  2021-01-08 North East and Yorkshire     66
## 1284  2021-01-09 North East and Yorkshire     49
## 1285  2021-01-10 North East and Yorkshire     77
## 1286  2021-01-11 North East and Yorkshire     78
## 1287  2021-01-12 North East and Yorkshire     59
## 1288  2021-01-13 North East and Yorkshire     64
## 1289  2021-01-14 North East and Yorkshire     60
## 1290  2021-01-15 North East and Yorkshire     57
## 1291  2021-01-16 North East and Yorkshire     48
## 1292  2021-01-17 North East and Yorkshire      7
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## 1294  2020-03-02               North West      0
## 1295  2020-03-03               North West      0
## 1296  2020-03-04               North West      0
## 1297  2020-03-05               North West      1
## 1298  2020-03-06               North West      0
## 1299  2020-03-07               North West      0
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## 1301  2020-03-09               North West      0
## 1302  2020-03-10               North West      0
## 1303  2020-03-11               North West      0
## 1304  2020-03-12               North West      2
## 1305  2020-03-13               North West      3
## 1306  2020-03-14               North West      1
## 1307  2020-03-15               North West      4
## 1308  2020-03-16               North West      2
## 1309  2020-03-17               North West      4
## 1310  2020-03-18               North West      6
## 1311  2020-03-19               North West      7
## 1312  2020-03-20               North West     10
## 1313  2020-03-21               North West     11
## 1314  2020-03-22               North West     13
## 1315  2020-03-23               North West     15
## 1316  2020-03-24               North West     21
## 1317  2020-03-25               North West     21
## 1318  2020-03-26               North West     29
## 1319  2020-03-27               North West     36
## 1320  2020-03-28               North West     28
## 1321  2020-03-29               North West     46
## 1322  2020-03-30               North West     67
## 1323  2020-03-31               North West     52
## 1324  2020-04-01               North West     86
## 1325  2020-04-02               North West     96
## 1326  2020-04-03               North West     95
## 1327  2020-04-04               North West     98
## 1328  2020-04-05               North West    102
## 1329  2020-04-06               North West    100
## 1330  2020-04-07               North West    136
## 1331  2020-04-08               North West    127
## 1332  2020-04-09               North West    119
## 1333  2020-04-10               North West    117
## 1334  2020-04-11               North West    138
## 1335  2020-04-12               North West    125
## 1336  2020-04-13               North West    130
## 1337  2020-04-14               North West    130
## 1338  2020-04-15               North West    114
## 1339  2020-04-16               North West    135
## 1340  2020-04-17               North West     98
## 1341  2020-04-18               North West    113
## 1342  2020-04-19               North West     71
## 1343  2020-04-20               North West     83
## 1344  2020-04-21               North West     76
## 1345  2020-04-22               North West     86
## 1346  2020-04-23               North West     85
## 1347  2020-04-24               North West     66
## 1348  2020-04-25               North West     66
## 1349  2020-04-26               North West     55
## 1350  2020-04-27               North West     54
## 1351  2020-04-28               North West     57
## 1352  2020-04-29               North West     63
## 1353  2020-04-30               North West     60
## 1354  2020-05-01               North West     45
## 1355  2020-05-02               North West     56
## 1356  2020-05-03               North West     55
## 1357  2020-05-04               North West     48
## 1358  2020-05-05               North West     48
## 1359  2020-05-06               North West     44
## 1360  2020-05-07               North West     49
## 1361  2020-05-08               North West     42
## 1362  2020-05-09               North West     31
## 1363  2020-05-10               North West     42
## 1364  2020-05-11               North West     35
## 1365  2020-05-12               North West     38
## 1366  2020-05-13               North West     25
## 1367  2020-05-14               North West     26
## 1368  2020-05-15               North West     33
## 1369  2020-05-16               North West     32
## 1370  2020-05-17               North West     24
## 1371  2020-05-18               North West     31
## 1372  2020-05-19               North West     35
## 1373  2020-05-20               North West     27
## 1374  2020-05-21               North West     28
## 1375  2020-05-22               North West     26
## 1376  2020-05-23               North West     31
## 1377  2020-05-24               North West     26
## 1378  2020-05-25               North West     31
## 1379  2020-05-26               North West     27
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## 1381  2020-05-28               North West     28
## 1382  2020-05-29               North West     20
## 1383  2020-05-30               North West     19
## 1384  2020-05-31               North West     13
## 1385  2020-06-01               North West     12
## 1386  2020-06-02               North West     27
## 1387  2020-06-03               North West     22
## 1388  2020-06-04               North West     22
## 1389  2020-06-05               North West     16
## 1390  2020-06-06               North West     26
## 1391  2020-06-07               North West     20
## 1392  2020-06-08               North West     23
## 1393  2020-06-09               North West     17
## 1394  2020-06-10               North West     16
## 1395  2020-06-11               North West     16
## 1396  2020-06-12               North West     11
## 1397  2020-06-13               North West     10
## 1398  2020-06-14               North West     15
## 1399  2020-06-15               North West     16
## 1400  2020-06-16               North West     16
## 1401  2020-06-17               North West     13
## 1402  2020-06-18               North West     14
## 1403  2020-06-19               North West      7
## 1404  2020-06-20               North West     11
## 1405  2020-06-21               North West      8
## 1406  2020-06-22               North West     11
## 1407  2020-06-23               North West     13
## 1408  2020-06-24               North West     13
## 1409  2020-06-25               North West     15
## 1410  2020-06-26               North West      6
## 1411  2020-06-27               North West      7
## 1412  2020-06-28               North West      9
## 1413  2020-06-29               North West      9
## 1414  2020-06-30               North West      7
## 1415  2020-07-01               North West      3
## 1416  2020-07-02               North West      6
## 1417  2020-07-03               North West      7
## 1418  2020-07-04               North West      4
## 1419  2020-07-05               North West      6
## 1420  2020-07-06               North West      9
## 1421  2020-07-07               North West      8
## 1422  2020-07-08               North West      5
## 1423  2020-07-09               North West     10
## 1424  2020-07-10               North West      2
## 1425  2020-07-11               North West      5
## 1426  2020-07-12               North West      0
## 1427  2020-07-13               North West      6
## 1428  2020-07-14               North West      4
## 1429  2020-07-15               North West      5
## 1430  2020-07-16               North West      2
## 1431  2020-07-17               North West      4
## 1432  2020-07-18               North West      5
## 1433  2020-07-19               North West      3
## 1434  2020-07-20               North West      0
## 1435  2020-07-21               North West      2
## 1436  2020-07-22               North West      3
## 1437  2020-07-23               North West      3
## 1438  2020-07-24               North West      1
## 1439  2020-07-25               North West      1
## 1440  2020-07-26               North West      3
## 1441  2020-07-27               North West      1
## 1442  2020-07-28               North West      1
## 1443  2020-07-29               North West      2
## 1444  2020-07-30               North West      2
## 1445  2020-07-31               North West      0
## 1446  2020-08-01               North West      2
## 1447  2020-08-02               North West      1
## 1448  2020-08-03               North West      8
## 1449  2020-08-04               North West      3
## 1450  2020-08-05               North West      2
## 1451  2020-08-06               North West      2
## 1452  2020-08-07               North West      2
## 1453  2020-08-08               North West      2
## 1454  2020-08-09               North West      3
## 1455  2020-08-10               North West      2
## 1456  2020-08-11               North West      3
## 1457  2020-08-12               North West      0
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## 1478  2020-09-02               North West      2
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## 1480  2020-09-04               North West      3
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## 1483  2020-09-07               North West      8
## 1484  2020-09-08               North West      6
## 1485  2020-09-09               North West      5
## 1486  2020-09-10               North West      5
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## 1509  2020-10-03               North West     15
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## 1966  2020-03-28               South West     21
## 1967  2020-03-29               South West     18
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## 2019  2020-05-20               South West      1
## 2020  2020-05-21               South West      9
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## 2052  2020-06-22               South West      1
## 2053  2020-06-23               South West      1
## 2054  2020-06-24               South West      1
## 2055  2020-06-25               South West      0
## 2056  2020-06-26               South West      3
## 2057  2020-06-27               South West      0
## 2058  2020-06-28               South West      0
## 2059  2020-06-29               South West      1
## 2060  2020-06-30               South West      0
## 2061  2020-07-01               South West      0
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## 2065  2020-07-05               South West      1
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## 2073  2020-07-13               South West      1
## 2074  2020-07-14               South West      0
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## 2087  2020-07-27               South West      0
## 2088  2020-07-28               South West      0
## 2089  2020-07-29               South West      0
## 2090  2020-07-30               South West      1
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## 2105  2020-08-14               South West      1
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## 2116  2020-08-25               South West      1
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## 2118  2020-08-27               South West      1
## 2119  2020-08-28               South West      0
## 2120  2020-08-29               South West      0
## 2121  2020-08-30               South West      0
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## 2129  2020-09-07               South West      0
## 2130  2020-09-08               South West      1
## 2131  2020-09-09               South West      0
## 2132  2020-09-10               South West      0
## 2133  2020-09-11               South West      0
## 2134  2020-09-12               South West      0
## 2135  2020-09-13               South West      1
## 2136  2020-09-14               South West      0
## 2137  2020-09-15               South West      0
## 2138  2020-09-16               South West      0
## 2139  2020-09-17               South West      1
## 2140  2020-09-18               South West      0
## 2141  2020-09-19               South West      0
## 2142  2020-09-20               South West      1
## 2143  2020-09-21               South West      0
## 2144  2020-09-22               South West      0
## 2145  2020-09-23               South West      0
## 2146  2020-09-24               South West      1
## 2147  2020-09-25               South West      0
## 2148  2020-09-26               South West      0
## 2149  2020-09-27               South West      0
## 2150  2020-09-28               South West      0
## 2151  2020-09-29               South West      0
## 2152  2020-09-30               South West      0
## 2153  2020-10-01               South West      0
## 2154  2020-10-02               South West      1
## 2155  2020-10-03               South West      0
## 2156  2020-10-04               South West      0
## 2157  2020-10-05               South West      0
## 2158  2020-10-06               South West      1
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## 2160  2020-10-08               South West      1
## 2161  2020-10-09               South West      1
## 2162  2020-10-10               South West      0
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## 2164  2020-10-12               South West      2
## 2165  2020-10-13               South West      0
## 2166  2020-10-14               South West      3
## 2167  2020-10-15               South West      1
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## 2170  2020-10-18               South West      2
## 2171  2020-10-19               South West      2
## 2172  2020-10-20               South West      3
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## 2175  2020-10-23               South West      5
## 2176  2020-10-24               South West      5
## 2177  2020-10-25               South West      5
## 2178  2020-10-26               South West      7
## 2179  2020-10-27               South West      6
## 2180  2020-10-28               South West      8
## 2181  2020-10-29               South West     11
## 2182  2020-10-30               South West      8
## 2183  2020-10-31               South West      4
## 2184  2020-11-01               South West      5
## 2185  2020-11-02               South West     11
## 2186  2020-11-03               South West      7
## 2187  2020-11-04               South West      8
## 2188  2020-11-05               South West      5
## 2189  2020-11-06               South West     11
## 2190  2020-11-07               South West     10
## 2191  2020-11-08               South West     10
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## 2193  2020-11-10               South West      6
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## 2196  2020-11-13               South West      9
## 2197  2020-11-14               South West      8
## 2198  2020-11-15               South West     16
## 2199  2020-11-16               South West     18
## 2200  2020-11-17               South West     17
## 2201  2020-11-18               South West     26
## 2202  2020-11-19               South West     15
## 2203  2020-11-20               South West     25
## 2204  2020-11-21               South West     25
## 2205  2020-11-22               South West     23
## 2206  2020-11-23               South West     14
## 2207  2020-11-24               South West     20
## 2208  2020-11-25               South West     25
## 2209  2020-11-26               South West     16
## 2210  2020-11-27               South West     21
## 2211  2020-11-28               South West     35
## 2212  2020-11-29               South West     15
## 2213  2020-11-30               South West     21
## 2214  2020-12-01               South West     19
## 2215  2020-12-02               South West     15
## 2216  2020-12-03               South West     14
## 2217  2020-12-04               South West     20
## 2218  2020-12-05               South West     17
## 2219  2020-12-06               South West     13
## 2220  2020-12-07               South West     14
## 2221  2020-12-08               South West     19
## 2222  2020-12-09               South West     21
## 2223  2020-12-10               South West     20
## 2224  2020-12-11               South West     20
## 2225  2020-12-12               South West     15
## 2226  2020-12-13               South West     19
## 2227  2020-12-14               South West     20
## 2228  2020-12-15               South West     19
## 2229  2020-12-16               South West      9
## 2230  2020-12-17               South West     25
## 2231  2020-12-18               South West     10
## 2232  2020-12-19               South West     22
## 2233  2020-12-20               South West     19
## 2234  2020-12-21               South West     21
## 2235  2020-12-22               South West     10
## 2236  2020-12-23               South West     16
## 2237  2020-12-24               South West     18
## 2238  2020-12-25               South West     19
## 2239  2020-12-26               South West     24
## 2240  2020-12-27               South West     24
## 2241  2020-12-28               South West     20
## 2242  2020-12-29               South West     20
## 2243  2020-12-30               South West     14
## 2244  2020-12-31               South West     26
## 2245  2021-01-01               South West     28
## 2246  2021-01-02               South West     22
## 2247  2021-01-03               South West     24
## 2248  2021-01-04               South West     30
## 2249  2021-01-05               South West     30
## 2250  2021-01-06               South West     24
## 2251  2021-01-07               South West     29
## 2252  2021-01-08               South West     33
## 2253  2021-01-09               South West     26
## 2254  2021-01-10               South West     30
## 2255  2021-01-11               South West     35
## 2256  2021-01-12               South West     46
## 2257  2021-01-13               South West     40
## 2258  2021-01-14               South West     26
## 2259  2021-01-15               South West     25
## 2260  2021-01-16               South West     21
## 2261  2021-01-17               South West      2

1.5 Completion date

We extract the completion date from the NHS Pathways file timestamp:


database_date <- attr(x, "timestamp")
database_date
## [1] "2021-01-18"

The completion date of the NHS Pathways data is Monday 18 Jan 2021.

1.6 Auxiliary functions

These are functions which will be used further in the analyses.

Function to estimate the generalised R-squared as the proportion of deviance explained by a given model:


## Function to calculate R2 for Poisson model
## not adjusted for model complexity but all models have the same DF here

Rsq <- function(x) {
  1 - (x$deviance / x$null.deviance)
}

Function to extract growth rates per region as well as halving times, and the associated 95% confidence intervals:


## function to extract the coefficients, find the level of the intercept,
## reconstruct the values of r, get confidence intervals

get_r <- function(model) {
  ##  extract coefficients and conf int
  out <- data.frame(r = coef(model))  %>%
    rownames_to_column("var") %>% 
    cbind(confint(model)) %>%
    filter(!grepl("day_of_week", var)) %>% 
    filter(grepl("day", var)) %>%
    rename(lower_95 = "2.5 %",
           upper_95 = "97.5 %") %>%
    mutate(var = sub("day:", "", var))
  
  ## reconstruct values: intercept + region-coefficient
  for (i in 2:nrow(out)) {
    out[i, -1] <- out[1, -1] + out[i, -1]
  }
  
  ## find the name of the intercept, restore regions names
  out <- out %>%
    mutate(nhs_region = model$xlevels$nhs_region) %>%
    select(nhs_region, everything(), -var)
  
  ## find halving times
  halving <- log(0.5) / out[,-1] %>%
    rename(halving_t = r,
           halving_t_lower_95 = lower_95,
           halving_t_upper_95 = upper_95)
  
  ## set halving times with exclusion intervals to NA
  no_halving <- out$lower_95 < 0 & out$upper_95 > 0
  halving[no_halving, ] <- NA_real_
  
  ## return all data
  cbind(out, halving)
  
}

Functions used in the correlation analysis between NHS Pathways reports and deaths:

## Function to calculate Pearson's correlation between deaths and lagged
## reports. Note that `pearson` can be replaced with `spearman` for rank
## correlation.

getcor <- function(x, ndx) {
  return(cor(x$deaths[ndx],
             x$note_lag[ndx],
             use = "complete.obs",
             method = "pearson"))
}

## Catch if sample size throws an error
getcor2 <- possibly(getcor, otherwise = NA)

getboot <- function(x) {
  result <- boot::boot.ci(boot::boot(x, getcor2, R = 1000), 
                           type = "bca")
  return(data.frame(n = sum(!is.na(x$note_lag) & !is.na(x$deaths)),
                    r = result$t0,
                    r_low = result$bca[4],
                    r_hi = result$bca[5]))
}

Function to classify the day of the week into weekend, Monday, and the rest:


## Fn to add day of week
day_of_week <- function(df) {
  df %>% 
    dplyr::mutate(day_of_week = lubridate::wday(date, label = TRUE)) %>% 
    dplyr::mutate(day_of_week = dplyr::case_when(
      day_of_week %in% c("Sat", "Sun") ~ "weekend",
      day_of_week %in% c("Mon") ~ "monday",
      !(day_of_week %in% c("Sat", "Sun", "Mon")) ~ "rest_of_week"
    ) %>% 
      factor(levels = c("rest_of_week", "monday", "weekend")))
}

Custom color palettes, color scales, and vectors of colors:


pal <- c("#006212",
         "#ae3cab",
         "#00db90",
         "#960c00",
         "#55aaff",
         "#ff7e78",
         "#00388d")

age.pal <- viridis::viridis(3,begin = 0.1, end = 0.7)

3 Comparison with deaths time series

3.1 Outline

We want to explore the correlation between NHS Pathways reports and deaths, and assess the potential for reports to be used as an early warning system for disease resurgence.

Death data are publically available. We truncate the time series to avoid bias from reporting delay - we assume a conservative delay of three weeks.

3.2 Lagged correlation

We calculate Pearson’s correlation coefficient between deaths and NHS Pathways notifications using different lags. Confidence intervals are obtained using bootstrap. Note that results were also confirmed using Spearman’s rank correlation.

First we join the NHS Pathways and death data, and aggregate over all England:

## truncate death data for reporting delay
trunc_date <- max(dth$date_report) - delay_max

dth_trunc <- dth %>%
  rename(date = date_report) %>%
  filter(date <= trunc_date) 

## join with notification data
all_data <- x %>% 
  filter(!is.na(nhs_region)) %>%
  group_by(date, nhs_region) %>%
  summarise(count = sum(count, na.rm = T)) %>%
  ungroup %>%
  inner_join(dth_trunc,
             by = c("date","nhs_region"))

all_tot <- all_data %>%
  group_by(date) %>%
  summarise(count = sum(count, na.rm = TRUE),
            deaths = sum(deaths, na.rm = TRUE)) 

We calculate correlation with lagged NHS Pathways reports from 0 to 30 days behind deaths:


## Calculate all correlations + bootstrap CIs
lag_cor <- data.frame()
for (i in 0:30) {
  
  ## lag reports
  summary <- all_tot %>% 
    mutate(note_lag = lag(count, i)) %>%
    ## calculate rank correlation and bootstrap CI
    getboot(.) %>%
    mutate(lag = i)

  lag_cor <- bind_rows(lag_cor, summary)
}

cor_vs_lag <- ggplot(lag_cor, aes(lag, r)) +
  theme_bw() +
  geom_ribbon(aes(ymin = r_low, ymax = r_hi), alpha = 0.2) +
  geom_hline(yintercept = 0, lty = "longdash") +
  geom_point() +
  geom_line() +
  labs(x = "Lag between NHS pathways and death data (days)",
       y = "Pearson's correlation") +
  large_txt
cor_vs_lag


l_opt <- which.max(lag_cor$r)

This analysis suggests that the best lag is 16 days. We then compare and plot the number of deaths reported against the number of NHS Pathways reports lagged by 16 days.


all_tot <- all_tot %>%
  rename(date_death = date) %>%
  mutate(note_lag = lag(count, lag_cor$lag[l_opt]),
         note_lag_c = (note_lag - mean(note_lag, na.rm = T)),
         date_note = lag(date_death,16))

lag_mod <- glm(deaths ~ note_lag, data = all_tot, family = "quasipoisson")

summary(lag_mod)
## 
## Call:
## glm(formula = deaths ~ note_lag, family = "quasipoisson", data = all_tot)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -14.688  -11.988   -4.324    8.085   22.626  
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 4.684e+00  6.418e-02   72.98   <2e-16 ***
## note_lag    1.556e-05  9.377e-07   16.59   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for quasipoisson family taken to be 110.3369)
## 
##     Null deviance: 52410  on 268  degrees of freedom
## Residual deviance: 30725  on 267  degrees of freedom
##   (16 observations deleted due to missingness)
## AIC: NA
## 
## Number of Fisher Scoring iterations: 5

exp(coefficients(lag_mod))
## (Intercept)    note_lag 
##  108.173349    1.000016
exp(confint(lag_mod))
##                 2.5 %     97.5 %
## (Intercept) 95.168588 122.401825
## note_lag     1.000014   1.000017

Rsq(lag_mod)
## [1] 0.4137481

mod_fit <- as.data.frame(predict(lag_mod, type = "link", se.fit = TRUE)[1:2])

all_tot_pred <- 
  all_tot %>%
  filter(!is.na(note_lag)) %>%
  mutate(pred = mod_fit$fit,
         pred.se = mod_fit$se.fit,
         low = exp(pred - 1.96*pred.se),
         hi = exp(pred + 1.96*pred.se))


glm_fit <- all_tot_pred %>% 
    filter(!is.na(note_lag)) %>%
  ggplot(aes(x = note_lag, y = deaths)) +
  geom_point() + 
  geom_line(aes(y = exp(pred))) + 
  geom_ribbon(aes(ymin = low, ymax = hi), alpha = 0.3, col = "grey") +
  theme_bw() +
  labs(y = "Daily number of\ndeaths reported",
       x = "Daily number of NHS Pathways reports") +
  large_txt

glm_fit

4 Supplementary figures

4.1 Serial interval distribution

This is a comparison of gamma versus lognormal distribution for the serial interval used to convert r to R in our analysis. Both distributions are parameterised with mean 4.7 and standard deviation 2.9.

SI_param <- epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale, w = 0.5)

SI_distribution2 <- distcrete::distcrete("lnorm", interval = 1,
                                        meanlog = log(4.7),
                                        sdlog = log(2.9), w = 0.5)

SI_dist1 <- data.frame(x = SI_distribution$r(1e5)) 
SI_dist1 <- count(SI_dist1, x) %>%
    ggplot() +
    geom_col(aes(x = x, y = n)) +
    labs(x = "Serial interval (days)", y = "Frequency") +
    scale_x_continuous(breaks = seq(0, 30, 5)) +
    theme_bw()

SI_dist2 <- data.frame(x = SI_distribution2$r(1e5)) 
SI_dist2 <- count(SI_dist2, x) %>%
    ggplot() +
    geom_col(aes(x = x, y = n)) +
    labs(x = "Serial interval (days)", y = "Frequency") +
    scale_x_continuous(breaks = seq(0, 200, 20), limits = c(0, 200)) +
    theme_bw()


ggpubr::ggarrange(SI_dist1,
                  SI_dist2,
                  nrow = 1,
                  labels = "AUTO") 

4.2 Sensitivity analysis - 7 or 21 days moving window

We reproduce the window analysis with either a 7 or 21 days window for sensitivity purposes.

First with the 7 days window:

## set moving time window (1/2/3 weeks)
w <- 7

# create empty df
r_all_sliding_7days <- NULL

## make data for model
x_model_all_moving <- x %>%
  filter(!is.na(nhs_region)) %>% 
  group_by(date, nhs_region) %>%
  summarise(n = sum(count)) 

unique_dates <- unique(x_model_all_moving$date)

for (i in 1:(length(unique_dates) - w)) {
  
  date_i <- unique_dates[i]
  
  date_i_max <- date_i + w
  
  model_data <- x_model_all_moving %>%
    filter(date >= date_i & date < date_i_max) %>%
    mutate(day = as.integer(date - date_i)) %>% 
    day_of_week()
  
  
  mod <- glm(n ~ day * nhs_region + day_of_week,
             data = model_data,
             family = 'quasipoisson')
  
  # get growth rate
  r <- get_r(mod)
  r$w_min <- date_i
  r$w_max <- date_i_max
  
  # combine all estimates
  r_all_sliding_7days <- bind_rows(r_all_sliding_7days, r)
  
}

#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale,
                                        w = 0.5)

#convert growth rates r to R0
r_all_sliding_7days <- r_all_sliding_7days %>%
  mutate(R = epitrix::r2R0(r, SI_distribution),
         R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
         R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))
# plot
plot_growth <-
  r_all_sliding_7days %>%
  ggplot(aes(x = w_max, y = r)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 0, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated daily growth rate (r)") +
  scale_colour_manual(values = pal)
plot_R <- r_all_sliding_7days %>%
  ggplot(aes(x = w_max, y = R)) +
  geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 1, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated effective reproduction\nnumber (Re)") +
  scale_colour_manual(values = pal)

R <- r_all_sliding_7days %>%
  mutate(lower_95 = R_lower_95, 
         upper_95 = R_upper_95,
         value = R,
         measure = "R",
         reference = 1)

r_R <- r_all_sliding_7days %>%
  mutate(measure = "r",
         value = r,
         reference = 0) %>%
  bind_rows(R)

r_R_7 <- r_R %>%
  ggplot(aes(x = w_max, y = value)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(aes(yintercept = reference), linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0,0, "cm"),
        strip.background = element_blank(),
        strip.placement = "outside"
  ) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "", y = "") +
  scale_colour_manual(values = pal) +
  facet_grid(rows = vars(measure),
             scales = "free_y",
             switch = "y",
             labeller = as_labeller(c(r = "Daily growth rate (r)",
                                      R = "Effective reproduction\nnumber (Re)")))

Then with the 21 days window:

## set moving time window (1/2/3 weeks)
w <- 21

# create empty df
r_all_sliding_21days <- NULL

## make data for model
x_model_all_moving <- x %>%
  filter(!is.na(nhs_region)) %>% 
  group_by(date, nhs_region) %>%
  summarise(n = sum(count)) 

unique_dates <- unique(x_model_all_moving$date)

for (i in 1:(length(unique_dates) - w)) {
  
  date_i <- unique_dates[i]
  
  date_i_max <- date_i + w
  
  model_data <- x_model_all_moving %>%
    filter(date >= date_i & date < date_i_max) %>%
    mutate(day = as.integer(date - date_i)) %>% 
    day_of_week()
  
  
  mod <- glm(n ~ day * nhs_region + day_of_week,
             data = model_data,
             family = 'quasipoisson')
  
  # get growth rate
  r <- get_r(mod)
  r$w_min <- date_i
  r$w_max <- date_i_max
  
  # combine all estimates
  r_all_sliding_21days <- bind_rows(r_all_sliding_21days, r)
  
}

#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale,
                                        w = 0.5)

#convert growth rates r to R0
r_all_sliding_21days <- r_all_sliding_21days %>%
  mutate(R = epitrix::r2R0(r, SI_distribution),
         R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
         R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))
# plot
plot_growth <-
  r_all_sliding_21days %>%
  ggplot(aes(x = w_max, y = r)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 0, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated daily growth rate (r)") +
  scale_colour_manual(values = pal)
# plot
plot_R <-
  r_all_sliding_21days %>%
  ggplot(aes(x = w_max, y = R)) +
  geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 1, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated effective reproduction\nnumber (Re)") +
  scale_colour_manual(values = pal)

R <- r_all_sliding_21days %>%
  mutate(lower_95 = R_lower_95, 
         upper_95 = R_upper_95,
         value = R,
         measure = "R",
         reference = 1)

r_R <- r_all_sliding_21days %>%
  mutate(measure = "r",
         value = r,
         reference = 0) %>%
  bind_rows(R)

r_R_21 <- r_R %>%
  ggplot(aes(x = w_max, y = value)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(aes(yintercept = reference), linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0,0, "cm"),
        strip.background = element_blank(),
        strip.placement = "outside"
  ) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "", y = "") +
  scale_colour_manual(values = pal) +
  facet_grid(rows = vars(measure),
             scales = "free_y",
             switch = "y",
             labeller = as_labeller(c(r = "Daily growth rate (r)",
                                      R = "Effective reproduction\nnumber (Re)")))

And we combine both outputs into a single plot:


ggpubr::ggarrange(r_R_7,
                  r_R_21,
                  nrow = 2,
                  labels = "AUTO",
                  common.legend = TRUE,
                  legend = "bottom") 

4.3 Correlation between NHS Pathways reports and deaths by NHS region


lag_cor_reg <- data.frame()

for (i in 0:30) {

  summary <-
    all_data %>%
    group_by(nhs_region) %>%
    mutate(note_lag = lag(count, i)) %>%
    ## calculate rank correlation and bootstrap CI for each region
    group_modify(~getboot(.x)) %>%
    mutate(lag = i)
  
  lag_cor_reg <- bind_rows(lag_cor_reg, summary)
}

cor_vs_lag_reg <- 
lag_cor_reg %>%
ggplot(aes(lag, r, col = nhs_region)) +
  geom_hline(yintercept = 0, lty = "longdash") +
  geom_ribbon(aes(ymin = r_low, ymax = r_hi, col = NULL, fill = nhs_region), alpha = 0.2) +
  geom_point() +
  geom_line() +
  facet_wrap(~nhs_region) +
  scale_color_manual(values = pal) +
  scale_fill_manual(values = pal, guide = F) +  
  theme_bw() +
  labs(x = "Lag between NHS pathways and death data (days)", y = "Pearson's correlation", col = "NHS region") +
  theme(legend.position = "bottom") +
  guides(color = guide_legend(override.aes = list(fill = NA)))

cor_vs_lag_reg

5 Export data

We save the tables created during our analysis:


if (!dir.exists("excel_tables")) {
  dir.create("excel_tables")
}


## list all tables, and loop over export
tables_to_export <- c("r_all_sliding", "lag_cor")

for (e in tables_to_export) {
  rio::export(get(e),
              file.path("excel_tables",
                        paste0(e, ".xlsx")))
}

## also export result from regression on lagged data 
rio::export(lag_mod, file.path("excel_tables", "lag_mod.rds"))

6 System information

6.1 Outline

The following information documents the system on which the document was compiled.

6.2 System

This provides information on the operating system.

Sys.info()
##                                                                                              sysname 
##                                                                                             "Darwin" 
##                                                                                              release 
##                                                                                             "19.6.0" 
##                                                                                              version 
## "Darwin Kernel Version 19.6.0: Thu Oct 29 22:56:45 PDT 2020; root:xnu-6153.141.2.2~1/RELEASE_X86_64" 
##                                                                                             nodename 
##                                                                            "Mac-1611053245850.local" 
##                                                                                              machine 
##                                                                                             "x86_64" 
##                                                                                                login 
##                                                                                               "root" 
##                                                                                                 user 
##                                                                                             "runner" 
##                                                                                       effective_user 
##                                                                                             "runner"

6.3 R environment

This provides information on the version of R used:

R.version
##                _                           
## platform       x86_64-apple-darwin17.0     
## arch           x86_64                      
## os             darwin17.0                  
## system         x86_64, darwin17.0          
## status                                     
## major          4                           
## minor          0.3                         
## year           2020                        
## month          10                          
## day            10                          
## svn rev        79318                       
## language       R                           
## version.string R version 4.0.3 (2020-10-10)
## nickname       Bunny-Wunnies Freak Out

6.4 R packages

This provides information on the packages used:

sessionInfo()
## R version 4.0.3 (2020-10-10)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.7
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] ggnewscale_0.4.5     ggpubr_0.4.0         lubridate_1.7.9.2   
##  [4] chngpt_2020.10-12    cyphr_1.1.0          DT_0.17             
##  [7] kableExtra_1.3.1     janitor_2.1.0        remotes_2.2.0       
## [10] projections_0.5.2    earlyR_0.0.5         epitrix_0.2.2       
## [13] distcrete_1.0.3      incidence_1.7.3      rio_0.5.16          
## [16] reshape2_1.4.4       rvest_0.3.6          xml2_1.3.2          
## [19] linelist_0.0.40.9000 forcats_0.5.0        stringr_1.4.0       
## [22] dplyr_1.0.3          purrr_0.3.4          readr_1.4.0         
## [25] tidyr_1.1.2          tibble_3.0.5         ggplot2_3.3.3       
## [28] tidyverse_1.3.0      here_1.0.1           reportfactory_0.0.5 
## 
## loaded via a namespace (and not attached):
##  [1] minqa_1.2.4       colorspace_2.0-0  selectr_0.4-2     ggsignif_0.6.0   
##  [5] ellipsis_0.3.1    rprojroot_2.0.2   snakecase_0.11.0  fs_1.5.0         
##  [9] rstudioapi_0.13   farver_2.0.3      fansi_0.4.2       splines_4.0.3    
## [13] knitr_1.30        jsonlite_1.7.2    nloptr_1.2.2.2    broom_0.7.3      
## [17] dbplyr_2.0.0      compiler_4.0.3    httr_1.4.2        backports_1.2.1  
## [21] assertthat_0.2.1  Matrix_1.2-18     cli_2.2.0         htmltools_0.5.1  
## [25] tools_4.0.3       gtable_0.3.0      glue_1.4.2        Rcpp_1.0.6       
## [29] carData_3.0-4     cellranger_1.1.0  vctrs_0.3.6       nlme_3.1-149     
## [33] matchmaker_0.1.1  crosstalk_1.1.1   xfun_0.20         ps_1.5.0         
## [37] openxlsx_4.2.3    lme4_1.1-26       lifecycle_0.2.0   statmod_1.4.35   
## [41] rstatix_0.6.0     MASS_7.3-53       scales_1.1.1      hms_1.0.0        
## [45] parallel_4.0.3    sodium_1.1        yaml_2.2.1        curl_4.3         
## [49] gridExtra_2.3     stringi_1.5.3     kyotil_2020.10-12 boot_1.3-25      
## [53] zip_2.1.1         rlang_0.4.10      pkgconfig_2.0.3   evaluate_0.14    
## [57] lattice_0.20-41   labeling_0.4.2    htmlwidgets_1.5.3 cowplot_1.1.1    
## [61] tidyselect_1.1.0  plyr_1.8.6        magrittr_2.0.1    R6_2.5.0         
## [65] generics_0.1.0    DBI_1.1.1         pillar_1.4.7      haven_2.3.1      
## [69] foreign_0.8-80    withr_2.4.0       mgcv_1.8-33       survival_3.2-7   
## [73] abind_1.4-5       modelr_0.1.8      crayon_1.3.4      car_3.0-10       
## [77] utf8_1.1.4        rmarkdown_2.6     viridis_0.5.1     grid_4.0.3       
## [81] readxl_1.3.1      data.table_1.13.6 reprex_0.3.0      digest_0.6.27    
## [85] webshot_0.5.2     munsell_0.5.0     viridisLite_0.3.0